BRCA
Daniel Kaplan
May 29, 2014
Resources
BRCA
But keep in mind that it’s a mutation in BRCA that’s associated with an increased risk of cancer. These data are not comparing normal and mutation.
Looking for the relationship between the BRCA gene and cancer.
Paul Overvoorde provided a file from the NCI site. [NEED MORE DETAILS]. It gives gene expression levels in 60 subjects.
fileName <- "/Users/kaplan/Downloads/filesandlinks/nci60_RNA__Agilent_mRNA_log2.txt/nci60_RNA__Agilent_mRNA_log2.txt"
geneExpress <- read.table( fileName, head=TRUE )geneNames <- as.character(geneExpress$Probe)Find the ones with a name indicating BRC
keepers <- filter(geneExpress, grepl("BRC", as.character(Probe)))
nrow(keepers)## [1] 4There are 4 such genes.
Transform from a wide format (where each column is a patient) to a narrow format (where columns are cell-line, probe, measurement).
express <- melt(keepers,variable='Cell.Line.Name',value.name='expression')## Using Experiment, Name, symbol, Probe, Name.1 as id variablesallgenes <- melt(geneExpress,variable='Cell.Line.Name',value.name='expression' )## Using Experiment, Name, symbol, Probe, Name.1 as id variablesThe information about the cell lines:
- Note, the punctuation is different in cellLineData than in express, so merging doesn’t work. Fix that by changing the punctuation.
cellLineFile <- "/Users/kaplan/KaplanFiles/DCF-2014/CaseStudies/NCI-gene/nci60_cellline_metadata.csv"
cellLineData <- read.csv( cellLineFile, head=TRUE)
# There are different punctuations in the Cell.Line.Names for express and cellLineData.
cellLineData <- mutate(cellLineData, Cell.Line.Name=sub(":",'.',Cell.Line.Name))
both <- inner_join(express , cellLineData)## Joining by: "Cell.Line.Name"bothall <- inner_join(allgenes, cellLineData)## Joining by: "Cell.Line.Name"Construct the table for BRCA1
origs <- c('BRCA1','DTX3L',"BID","CALU","BFAR", "NONO")
top100 <- c('ACTG2' , 'SULF1' , 'COL3A1' , 'IGFBP5' , 'SLC24A3' , 'COL1A2' , 'LUM' , 'SPARC' , 'POSTN' , 'CXCL1' , 'A_23_P37685' , 'MGC16121' , 'UCHL1' , 'A_23_P203120' , 'ALDH2' , 'DCN' , 'DPYSL3' , 'CPXM2' , 'WISP1' , 'CDKN2A' , 'FEZ1' , 'CBS' , 'A_24_P372189' , 'CDCP1' , 'C10orf58' , 'CNN1' , 'A_32_P74409' , 'SYNPO2' , 'CDCP1' , 'WNT5A' , 'A_23_P305292' , 'KIAA0746' , 'COL1A1' , 'CDH11' , 'A_24_P299474' , 'GPR110' , 'A_23_P36226' , 'A_32_P214011' , 'A_23_P217901' , 'SPOCK1' , 'ACTA2' , 'KRT19' , 'A_24_P563966' , 'KRT17' , 'CXCL12' , 'KCNG1' , 'HSPB2' , 'VCX2' , 'FAP' , 'MRVI1' , 'TSHZ3' , 'ADAMTS4' , 'COL3A1' , 'OLFML3' , 'IFITM1' , 'RIMS2' , 'C19orf33' , 'BST2' , 'DPYSL3' , 'C11orf41' , 'VCX' , 'C5orf23' , 'CSTA' , 'ROBO1' , 'FOXD1' , 'IGFBP5' , 'CD248' , 'MX1' , 'ZNF469' , 'PLAC8' , 'ADFP' , 'APCDD1L' , 'CDH13' , 'CTHRC1' , 'SAA1' , 'A_32_P55241' , 'TMEM98' , 'COX7A1' , 'CST6' , 'A_23_P206741' , 'FAM101B' , 'A_32_P96752' , 'FKBP10' , 'BDKRB1' , 'A_24_P691826' , 'A_24_P887857' , 'VCX3A' , 'PCSK9' , 'ADAMTS5' , 'CTAG1A' , 'SIPA1L2' , 'A_24_P828496' , 'ROBO3' , 'G0S2' , 'KCNMA1' , 'ITGA8' , 'PLAC8' , 'PRAME' , 'PTGIS' , 'MAGEA2B' )
probeSet <- c(origs, top100)
res <- list()
for (probe in probeSet) {
filter(bothall, Probe==probe) %>%
group_by(tissue.of.origin) %>%
summarize(ave=mean(expression),stderr=sd(expression)/sqrt(n())) -> tmp
tmp$tissue.of.origin <- with(tmp,reorder(tissue.of.origin,-ave))
res[[probe]] <- tmp
}Fres <- data.frame( probe=character(length(probeSet)), F=NA, p=NA,
stringsAsFactors=FALSE)
for (probe in probeSet) {
P1 <- ggplot(data=res[[probe]], aes(x=tissue.of.origin,y=ave,color=tissue.of.origin))
P2 <- P1 +
geom_bar(stat='identity',position='dodge',alpha=0.2,color='gray') +
geom_errorbar(aes(ymax=ave+2*stderr,ymin=ave-2*stderr),
width=0.2,position=position_dodge(width=0.8))
raw <- filter(bothall, Probe==probe)
P3 <- P2 + geom_point(data=raw,
position=position_jitter(width=0.15),
aes(y=expression),alpha=.5)
print(P3 + ggtitle(probe) + xlab('Tissue type') +
ylab('Expression level (log2)') +
theme_tufte() + coord_flip())
tmp <- anova(lm(expression ~ tissue.of.origin, data=raw))
print(tmp)
Fres[which(probe == probeSet),] <- list(probe=probe, F=tmp[1,4], p=tmp[1,5] )
}
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 10.8 1.35 4.1 0.00079 ***
## Residuals 51 16.8 0.33
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 34 4.25 3.41 0.0015 **
## Residuals 111 138 1.24
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 20 2.54 0.78 0.62
## Residuals 111 363 3.27
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 37.5 4.68 7.03 3.2e-06 ***
## Residuals 51 34.0 0.67
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 28.4 3.55 1.87 0.072 .
## Residuals 111 211.0 1.90
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 4.3 0.538 1.06 0.4
## Residuals 111 56.4 0.508
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 155 19.32 2.9 0.0096 **
## Residuals 51 340 6.66
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 191 23.87 3.08 0.0065 **
## Residuals 51 395 7.74
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 303 37.9 6.27 4.2e-07 ***
## Residuals 171 1035 6.0
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 649 81.1 17.1 <2e-16 ***
## Residuals 171 812 4.7
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 106 13.24 4.31 0.00015 ***
## Residuals 111 341 3.07
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 632 79.0 11.4 1e-11 ***
## Residuals 111 767 6.9
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 129 16.06 1.94 0.074 .
## Residuals 51 422 8.28
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 1060 132.4 11.6 3.5e-09 ***
## Residuals 51 584 11.5
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 61.9 7.74 1.75 0.11
## Residuals 51 225.0 4.41
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 562 70.3 5.39 6.2e-05 ***
## Residuals 51 665 13.0
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 43 5.42 0.76 0.63
## Residuals 51 361 7.09
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 117 14.65 3.85 0.0013 **
## Residuals 51 194 3.81
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 1214 151.7 7.26 2.2e-06 ***
## Residuals 51 1066 20.9
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 330 41.3 3.17 0.0054 **
## Residuals 51 664 13.0
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 575 71.8 7.39 7.5e-08 ***
## Residuals 111 1079 9.7
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 30.8 3.84 1.33 0.25
## Residuals 51 146.9 2.88
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 452 56.4 5.25 1.4e-05 ***
## Residuals 111 1193 10.8
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 30.3 3.79 1.06 0.41
## Residuals 51 182.4 3.58
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 85.4 10.67 4.05 3e-04 ***
## Residuals 111 292.4 2.63
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 368 46.0 2.6 0.012 *
## Residuals 111 1964 17.7
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 340 42.5 7.96 2e-08 ***
## Residuals 111 593 5.3
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 233 29.07 3.19 0.0027 **
## Residuals 111 1013 9.13
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 76.7 9.59 2.84 0.011 *
## Residuals 51 172.1 3.37
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 964 120.5 15.9 <2e-16 ***
## Residuals 171 1294 7.6
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 176 22.04 3.25 0.0046 **
## Residuals 51 346 6.78
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 235 29.41 4.15 0.00071 ***
## Residuals 51 361 7.08
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 241 30.11 3.98 0.001 ***
## Residuals 51 386 7.56
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 34.8 4.35 1.73 0.099 .
## Residuals 111 279.1 2.51
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 964 120.5 15.9 <2e-16 ***
## Residuals 171 1294 7.6
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 266 33.3 4.29 0.00054 ***
## Residuals 51 396 7.8
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 33.2 4.15 1.32 0.25
## Residuals 51 159.9 3.14
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 339 42.4 7.64 1.2e-06 ***
## Residuals 51 283 5.6
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 285 35.7 4.54 0.00033 ***
## Residuals 51 401 7.9
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 287 35.9 3.79 0.0015 **
## Residuals 51 483 9.5
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 480 60.0 6.11 1.6e-05 ***
## Residuals 51 501 9.8
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 196 24.52 4.67 3.5e-05 ***
## Residuals 171 899 5.25
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 44.6 5.57 2.29 0.035 *
## Residuals 51 124.2 2.44
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 148 18.55 3.45 0.003 **
## Residuals 51 274 5.38
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 279 34.9 2.78 0.012 *
## Residuals 51 640 12.5
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 396 49.4 5.65 3.8e-05 ***
## Residuals 51 446 8.7
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 101 12.60 1.69 0.12
## Residuals 51 381 7.47
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 1151 143.8 11.6 3.5e-09 ***
## Residuals 51 635 12.4
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 47.1 5.89 2.87 0.01 *
## Residuals 51 104.7 2.05
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 80.5 10.06 2 0.065 .
## Residuals 51 256.6 5.03
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 327 40.9 8.31 1.7e-09 ***
## Residuals 171 841 4.9
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 192 23.95 5.45 8.4e-06 ***
## Residuals 111 488 4.39
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 189 23.7 2.08 0.055 .
## Residuals 51 580 11.4
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 102 12.80 2.41 0.02 *
## Residuals 111 591 5.32
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 302 37.7 4.66 0.00026 ***
## Residuals 51 413 8.1
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 27 3.38 1.44 0.2
## Residuals 51 120 2.35
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 265 33.1 5.02 0.00013 ***
## Residuals 51 337 6.6
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 137 17.13 5.08 2.1e-05 ***
## Residuals 111 374 3.37
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 303 37.9 6.27 4.2e-07 ***
## Residuals 171 1035 6.0
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 82 10.23 2.21 0.031 *
## Residuals 111 513 4.62
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 292 36.5 3.21 0.005 **
## Residuals 51 580 11.4
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 59 7.31 1.62 0.12
## Residuals 171 773 4.52
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 1699 212.4 73.1 <2e-16 ***
## Residuals 111 322 2.9
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 193 24.1 2.02 0.063 .
## Residuals 51 610 12.0
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 452 56.4 5.25 1.4e-05 ***
## Residuals 111 1193 10.8
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 355 44.4 6.78 5e-06 ***
## Residuals 51 334 6.5
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 89 11.16 1.29 0.27
## Residuals 51 440 8.62
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 234 29.30 4.34 0.00049 ***
## Residuals 51 344 6.75
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 44 5.55 1.05 0.4
## Residuals 111 587 5.29
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 342 42.8 6.3 1e-06 ***
## Residuals 111 753 6.8
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 133 16.60 2.67 0.01 *
## Residuals 111 690 6.22
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 649 81.1 17.1 <2e-16 ***
## Residuals 171 812 4.7
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 12.4 1.55 0.83 0.58
## Residuals 51 95.2 1.87
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 41 5.07 0.49 0.86
## Residuals 51 530 10.40
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 209 26.18 4.07 0.00084 ***
## Residuals 51 328 6.43
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 467 58.4 5.4 9.4e-06 ***
## Residuals 111 1199 10.8
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 201 25.16 4.36 0.00047 ***
## Residuals 51 294 5.77
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 112 13.99 2.23 0.04 *
## Residuals 51 320 6.27
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 176 22.0 1.93 0.075 .
## Residuals 51 581 11.4
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 277 34.7 3.12 0.0061 **
## Residuals 51 567 11.1
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 194 24.27 3.51 0.0027 **
## Residuals 51 353 6.93
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 183 22.91 3.47 0.0029 **
## Residuals 51 337 6.61
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 425 53.1 6.49 6.5e-07 ***
## Residuals 111 909 8.2
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 97.4 12.17 4.61 0.00028 ***
## Residuals 51 134.6 2.64
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 379 47.3 6.6 6.9e-06 ***
## Residuals 51 366 7.2
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 52.3 6.53 2.34 0.032 *
## Residuals 51 142.6 2.80
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 312 39.0 4.74 5e-05 ***
## Residuals 111 913 8.2
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 24.1 3.01 0.59 0.78
## Residuals 51 259.3 5.08
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 306 38.2 7.87 8e-07 ***
## Residuals 51 248 4.9
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 300 37.5 3.99 0.00034 ***
## Residuals 111 1042 9.4
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 201 25.10 4.57 3e-04 ***
## Residuals 51 280 5.49
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 80 10.00 2.44 0.025 *
## Residuals 51 209 4.09
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 75 9.40 1.3 0.27
## Residuals 51 369 7.24
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 299 37.4 3.23 0.0048 **
## Residuals 51 590 11.6
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 263 32.8 4.5 0.00035 ***
## Residuals 51 372 7.3
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 161 20.1 1.42 0.21
## Residuals 51 723 14.2
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 36 4.51 0.72 0.67
## Residuals 51 320 6.27
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 95.9 11.99 2.48 0.023 *
## Residuals 51 246.1 4.83
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 55 6.87 1.98 0.052 .
## Residuals 171 594 3.47
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 329 41.1 2.3 0.035 *
## Residuals 51 911 17.9
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 777 97.1 21.3 <2e-16 ***
## Residuals 291 1325 4.6
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 7.3 0.917 0.68 0.7
## Residuals 51 68.3 1.339
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 467 58.4 5.4 9.4e-06 ***
## Residuals 111 1199 10.8
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 992 124 12.4 1.3e-12 ***
## Residuals 111 1107 10
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 235 29.4 6.26 1.1e-06 ***
## Residuals 111 522 4.7
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table
##
## Response: expression
## Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin 8 610 76.2 5.16 9.7e-05 ***
## Residuals 51 754 14.8
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Fres## probe F p
## 1 BRCA1 4.0983 7.890e-04
## 2 DTX3L 3.4102 1.533e-03
## 3 BID 0.7771 6.236e-01
## 4 CALU 7.0343 3.231e-06
## 5 BFAR 1.8667 7.232e-02
## 6 NONO 1.0584 3.975e-01
## 7 ACTG2 2.8988 9.650e-03
## 8 SULF1 3.0825 6.532e-03
## 9 COL3A1 6.2655 4.179e-07
## 10 IGFBP5 17.0880 1.569e-18
## 11 SLC24A3 4.3145 1.499e-04
## 12 COL1A2 11.4289 1.024e-11
## 13 LUM 1.9402 7.385e-02
## 14 SPARC 11.5583 3.469e-09
## 15 POSTN 1.7535 1.086e-01
## 16 CXCL1 5.3910 6.234e-05
## 17 A_23_P37685 0.7649 6.348e-01
## 18 MGC16121 3.8483 1.316e-03
## 19 UCHL1 7.2614 2.194e-06
## 20 A_23_P203120 3.1743 5.378e-03
## 21 ALDH2 7.3890 7.536e-08
## 22 DCN 1.3348 2.480e-01
## 23 DPYSL3 5.2497 1.393e-05
## 24 CPXM2 1.0587 4.063e-01
## 25 WISP1 4.0498 2.957e-04
## 26 CDKN2A 2.5982 1.215e-02
## 27 FEZ1 7.9552 2.007e-08
## 28 CBS 3.1855 2.730e-03
## 29 A_24_P372189 2.8430 1.087e-02
## 30 CDCP1 15.9243 1.931e-17
## 31 C10orf58 3.2515 4.569e-03
## 32 CNN1 4.1514 7.083e-04
## 33 A_32_P74409 3.9832 9.978e-04
## 34 SYNPO2 1.7293 9.930e-02
## 35 CDCP1 15.9243 1.931e-17
## 36 WNT5A 4.2884 5.370e-04
## 37 A_23_P305292 1.3233 2.534e-01
## 38 KIAA0746 7.6441 1.157e-06
## 39 COL1A1 4.5350 3.279e-04
## 40 CDH11 3.7883 1.489e-03
## 41 A_24_P299474 6.1116 1.642e-05
## 42 GPR110 4.6671 3.509e-05
## 43 A_23_P36226 2.2880 3.548e-02
## 44 A_32_P214011 3.4505 3.007e-03
## 45 A_23_P217901 2.7832 1.235e-02
## 46 SPOCK1 5.6526 3.815e-05
## 47 ACTA2 1.6859 1.246e-01
## 48 KRT19 11.5566 3.477e-09
## 49 A_24_P563966 2.8710 1.024e-02
## 50 KRT17 1.9999 6.518e-02
## 51 CXCL12 8.3059 1.730e-09
## 52 KCNG1 5.4515 8.395e-06
## 53 HSPB2 2.0831 5.474e-02
## 54 VCX2 2.4060 1.964e-02
## 55 FAP 4.6587 2.567e-04
## 56 MRVI1 1.4406 2.027e-01
## 57 TSHZ3 5.0165 1.276e-04
## 58 ADAMTS4 5.0838 2.116e-05
## 59 COL3A1 6.2655 4.179e-07
## 60 OLFML3 2.2144 3.148e-02
## 61 IFITM1 3.2112 4.975e-03
## 62 RIMS2 1.6186 1.227e-01
## 63 C19orf33 73.1020 1.086e-40
## 64 BST2 2.0157 6.306e-02
## 65 DPYSL3 5.2497 1.393e-05
## 66 C11orf41 6.7831 4.985e-06
## 67 VCX 1.2948 2.673e-01
## 68 C5orf23 4.3385 4.855e-04
## 69 CSTA 1.0498 4.037e-01
## 70 ROBO1 6.3004 1.029e-06
## 71 FOXD1 2.6687 1.018e-02
## 72 IGFBP5 17.0880 1.569e-18
## 73 CD248 0.8299 5.805e-01
## 74 MX1 0.4880 8.591e-01
## 75 ZNF469 4.0699 8.359e-04
## 76 PLAC8 5.4045 9.444e-06
## 77 ADFP 4.3579 4.670e-04
## 78 APCDD1L 2.2305 4.009e-02
## 79 CDH13 1.9299 7.544e-02
## 80 CTHRC1 3.1187 6.050e-03
## 81 SAA1 3.5052 2.682e-03
## 82 A_32_P55241 3.4672 2.904e-03
## 83 TMEM98 6.4920 6.451e-07
## 84 COX7A1 4.6121 2.814e-04
## 85 CST6 6.6011 6.853e-06
## 86 A_23_P206741 2.3369 3.197e-02
## 87 FAM101B 4.7423 5.028e-05
## 88 A_32_P96752 0.5924 7.796e-01
## 89 FKBP10 7.8690 7.999e-07
## 90 BDKRB1 3.9903 3.445e-04
## 91 A_24_P691826 4.5749 3.029e-04
## 92 A_24_P887857 2.4437 2.547e-02
## 93 VCX3A 1.2989 2.653e-01
## 94 PCSK9 3.2326 4.755e-03
## 95 ADAMTS5 4.5006 3.511e-04
## 96 CTAG1A 1.4210 2.105e-01
## 97 SIPA1L2 0.7184 6.743e-01
## 98 A_24_P828496 2.4844 2.335e-02
## 99 ROBO3 1.9795 5.168e-02
## 100 G0S2 2.2997 3.461e-02
## 101 KCNMA1 21.3184 1.992e-25
## 102 ITGA8 0.6849 7.027e-01
## 103 PLAC8 5.4045 9.444e-06
## 104 PRAME 12.4337 1.345e-12
## 105 PTGIS 6.2596 1.137e-06
## 106 MAGEA2B 5.1593 9.692e-05